If Harry decides not to go to Hogwarts, the main antagonist could be the Ministry of Magic. They might see Harry as a threat since he's trying to practice magic on his own without proper supervision. They could send Aurors after him to stop him from causing any chaos in the Muggle world or from becoming a powerful, unregulated wizard.
Hufflepuff is popular for fanfiction because it represents the underdog. In the books, Gryffindors, Slytherins, and Ravenclaws often get more spotlight. So, writers like to explore the Hufflepuffs' hidden stories. Their traits like loyalty, hard work, and kindness offer a lot of potential for interesting plotlines.
Well, it could be that Harry makes a different choice regarding his friends. Instead of befriending Ron and Hermione, he might choose to hang out with some of the other students who are often overlooked, such as Neville. This would change the dynamics of the group and how they face the various threats at Hogwarts. It could also lead to Neville developing more confidence earlier in the story because of Harry's influence.
It could be a new dark wizard who has been secretly plotting in the shadows. This wizard might be jealous of Harry's fame and power, and decides to make him disappear so that he can rise to power unopposed. He could have a group of followers who are experts in dark magic and are able to carry out his plan to make Harry vanish.
The Queen of Hearts would make a great main villain. Her tyrannical rule and quick temper in the original Wonderland story could be amplified in a fanfiction. She could be a powerful dark magic user who sees Harry as a threat to her rule and tries to stop him from achieving his goals in Wonderland.
Voldemort could be a great villain. Imagine if he somehow discovers a way to enter Logan's world and starts using his dark magic to enslave mutants. Logan and Harry would have to put aside their differences in fighting styles and beliefs to take on Voldemort.
It could be a new character created by the fanfiction author. Maybe a powerful wizard who was once shunned by the wizarding community and now wants revenge by stealing magic.
Perhaps an old enemy of Harry's family resurfaces. This villain might have a long - standing grudge against the Potters and sees turning Harry into a baby as a form of ultimate revenge. They could be using a spell that has been passed down through generations in their family, a spell that was created specifically to harm the Potters.
A dark wizard who has merged the dark arts with Wonderland's magic could be the main villain. He might have created some sort of dark Wonderland where all the creatures are under his control, and Harry has to break this control to restore balance.